coala

Coala is an R package for simulating biological sequences according to a given model of evolution. It can call a number of efficient simulators based on coalescent theory. All simulators can be combined with the program seq-gen to simulate finite site mutation models. Coala also directly imports the simulation results into R, and can calculate various summary statistics from the results.

Problems

If you encounter problems when using coala, please file a bug report or mail to coala-pkg (at) googlegroups.com.

Supported Simulators

The package supports the coalescent simulators ms, scrm and msms. All simulators can be combined with seq-gen to simulate finite sites mutation models. The programs msms and seq-gen must be installed manually. The R version of scrm should be installed automatically, and the R version ms if the package phyclust is installed.

Development

To follow or participate in the development of coala, please install the development version from GitHub using

devtools::install_github('statgenlmu/coala')

on Linux and OS X. This requires that you have devtools and a compiler or Xcode installed. Bug reports and pull request on GitHub are highly appreciated. The extending coala vignette contains information on how to create new summary statistics and add simulators to coala. The wiki also contains a few resources for developers.